Re: Problem installing PERL DBD::mysql

2006-08-14 Thread Niels Larsen

Connie,

I had the same error with another program recently, but probably the
fix for yours is the same: try compile zlib with -fPIC by adding
 -fPIC to CFLAGS in the Makefile.

Niels Larsen



Logg, Connie A. wrote:

Machine info:

[EMAIL PROTECTED] utils]$ uname -a
Linux snv1 2.6.9-34.0.2.ELsmp #1 SMP Fri Jun 30 10:32:04 EDT 2006 x86_64 x86_64 
x86_64 GNU/Linux
[EMAIL PROTECTED] utils]$ perl -v
This is perl, v5.8.8 built for x86_64-linux
[EMAIL PROTECTED] utils]$ more /etc/redhat-release
Red Hat Enterprise Linux WS release 4 (Nahant Update 4)


--
I am having a hard time installing DBD:mysql on 64 bit machine snv1.ultralight.org 


/usr/bin/perl MCPAN -e shell
CPAN install DBD::mysql

Dies with errors...so I decided to do it from the source, and it also 
complainshere is the output from the source install:

[EMAIL PROTECTED] DBD-mysql-3.0006]# /usr/bin/perl Makefile.PL I will use the 
following settings for compiling and testing:

  cflags(mysql_config) = -I/usr/local/include/mysql
  embedded  (mysql_config) =
  libs  (mysql_config) = -L/usr/local/lib/mysql -lmysqlclient -lz 
-lcrypt -lnsl -lm
  mysql_config  (guessed ) = mysql_config
  nocatchstderr (default ) = 0
  nofoundrows   (default ) = 0
  ssl   (guessed ) = 0
  testdb(default ) = test
  testhost  (default ) =
  testpassword  (default ) =
  testsocket(default ) =
  testuser  (default ) =

To change these settings, see 'perl Makefile.PL --help' and 'perldoc INSTALL'.

Using DBI 1.52 (for perl 5.008008 on x86_64-linux) installed in 
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux/auto/DBI/
Writing Makefile for DBD::mysql
[EMAIL PROTECTED] DBD-mysql-3.0006]#
[EMAIL PROTECTED] DBD-mysql-3.0006]# make
cc -c  -I/usr/lib/perl5/site_perl/5.8.8/x86_64-linux/auto/DBI 
-I/usr/local/include/mysql -DDBD_MYSQL_INSERT_ID_IS_GOO D -g  
-fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include 
-D_LARGEFILE_SOURCE -D_FILE_OFFSE
T_BITS=64 -I/usr/include/gdbm -O2   -DVERSION=\3.0006\ -DXS_VERSION=\3.0006\ 
-fpic -I/usr/lib/perl5/5.8.8/x86_64
-linux/CORE   dbdimp.c
cc -c  -I/usr/lib/perl5/site_perl/5.8.8/x86_64-linux/auto/DBI 
-I/usr/local/include/mysql -DDBD_MYSQL_INSERT_ID_IS_GOO D -g  
-fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include 
-D_LARGEFILE_SOURCE -D_FILE_OFFSE
T_BITS=64 -I/usr/include/gdbm -O2   -DVERSION=\3.0006\ -DXS_VERSION=\3.0006\ 
-fpic -I/usr/lib/perl5/5.8.8/x86_64
-linux/CORE   mysql.c
mysql.xs: In function `XS_DBD__mysql__GetInfo_dbd_mysql_get_info':
mysql.xs:647: warning: ignoring return value of `Perl_newSViv', declared with 
attribute warn_unused_result
mysql.xs:650: warning: ignoring return value of `Perl_newSViv', declared with 
attribute warn_unused_result
mysql.xs:653: warning: ignoring return value of `Perl_newSVpv', declared with attribute 
warn_unused_result Running Mkbootstrap for DBD::mysql () chmod 644 mysql.bs rm -f 
blib/arch/auto/DBD/mysql/mysql.so LD_RUN_PATH=/usr/local/lib/mysql 
/usr/bin/perl myld cc  -shared -L/usr/local/lib dbdimp.o mysql.o  -o blib/arch/aut
o/DBD/mysql/mysql.so\
   -L/usr/local/lib/mysql -lmysqlclient -lz -lcrypt -lnsl -lm   \

/usr/bin/ld: /usr/local/lib/libz.a(compress.o): relocation R_X86_64_32 against 
`a local symbol' can not be used when making a shared object; recompile with 
-fPIC
/usr/local/lib/libz.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [blib/arch/auto/DBD/mysql/mysql.so] Error 1

I have tried using -fPIC, but I think I do not know how to tell it to use that 
correctly. I assume it is passed with --cflags on the 'perl Makefile.PL' line, 
but I can't get that to work.

Can someone tell me the syntax on the 'perl Makefile.PL' line, or, what the 
problem is and how can I get DBD::mysql to load?

By the way, perl Makefile.PL --help gives me..
[EMAIL PROTECTED] DBD-mysql-3.0006]# perl -Makefile.PL --help

Usage: perl [switches] [--] [programfile] [arguments]
  -0[octal]   specify record separator (\0, if no argument)
  -a  autosplit mode with -n or -p (splits $_ into @F)
  -C[number/list] enables the listed Unicode features
  -c  check syntax only (runs BEGIN and CHECK blocks)
  -d[:debugger]   run program under debugger
  -D[number/list] set debugging flags (argument is a bit mask or alphabets)
  -e program  one line of program (several -e's allowed, omit programfile)
  -f  don't do $sitelib/sitecustomize.pl at startup
  -F/pattern/ split() pattern for -a switch (//'s are optional)
  -i[extension]   edit  files in place (makes backup if extension supplied)
  -Idirectory specify @INC/#include directory (several -I's allowed)
  -l[octal]   enable line ending processing, specifies line terminator
  -[mM][-]module  execute use/no module... before executing program
  -n  assume while () { ... } loop around program

Re: Problem installing PERL DBD::mysql

2006-08-14 Thread Niels Larsen

Yes .. and had to add it to jpeg-6b (on x86_64) to make that
work too.

Patrick Galbraith wrote:

Niels Larsen wrote:

Niels,

Do you mean in the Makefile for zlib?

Thanks!

Patrick


Connie,

I had the same error with another program recently, but probably the
fix for yours is the same: try compile zlib with -fPIC by adding
 -fPIC to CFLAGS in the Makefile.

Niels Larsen


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Re: fulltext indexing and query speeds?

2003-07-29 Thread Niels Larsen
Sergei,

Thank you for the nice help. 

 Try to experiment with bulk_insert_buffer variable. You need both big
 keycache and big bulk_insert_buffer.

I lowered key_buffer_size from 512M to 256M and increased bulk_insert_buffer_size
from 8M to 128M. 

 When MERGE tables will support fulltext searches you can use them to
 keep small table where you insert data, and from time to time move the
 data from it to the big one. Actually you can do it with UNION even now,
 but it's not nice solution at all.

Oh, I will do anything to make it work .. I will do unions between 50 selects 
if I must. I access MySQL via an abstracted perl api which I dont change, 
so I can live with awful things underneath if there is just a shiny surface. If 
unionizing doesnt slow fulltext search much, then I try that first.

Will a future MySQL version combine the current nice and fast word-search 
with ability to add data in finite time? I saw Make all operations with FULLTEXT
index faster on the TODO list .. are you able to say what is in the pipe? 

Greetings, Niels L

Bioinformatics Research Center (BIRC)
Aarhus University
Hoegh Guldbergsgade 10
DK 8000 Aarhus C
Denmark


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fulltext indexing and query speeds?

2003-07-28 Thread Niels Larsen
Greetings,

Do anyone know where to find a description of how fulltext indexing 
and query speeds depend on data volume? I have 30-40 gb of text 
distributed across 30-40 million entries, a medium size database I 
suppose. But I have not even been able to test a query yet, because
indexing is on its second day. Which I think cant be right. I will come 
up with the details if anyone asks, but how long is indexing supposed
to take on different amounts of data? if there is a way to predict how 
long it will take, then that might work; then we may simply buy a 
machine do nothing but indexing .. assuming the boolean mode
queries finish in interactive time, ie seconds, not minutes. I use v.
4.0.12, but will happily upgrade if indexing becomes faster. 

Niels L



Niels Larsen, Associate Professor
Bioinformatics Research Center (BIRC)
Aarhus University
Hoegh Guldbergsgade 10
DK 8000 Aarhus C
Denmark




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